FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound Struct Reference

One target compound for the FeatureFinderAlgorithmMetaboIdent assay library. More...

#include <OpenMS/FEATUREFINDER/FeatureFinderAlgorithmMetaboIdent.h>

Collaboration diagram for FeatureFinderAlgorithmMetaboIdent::FeatureFinderMetaboIdentCompound:

Public Member Functions
	FeatureFinderMetaboIdentCompound (const std::string &_name, const std::string &_formula, double _mass, const std::vector< int > &_charges, const std::vector< double > &_rts, const std::vector< double > &_rt_ranges, const std::vector< double > &_iso_distrib, const std::vector< double > &_ion_mobilities={}, const std::string &_adduct="")
	Construct a target compound by aggregating its identification data.
const std::string &	getName () const
	Return the target name.
const std::string &	getFormula () const
	Return the molecular formula (may be empty if only mass was provided).
double	getMass () const
	Return the monoisotopic mass; <= 0 means "compute from @c formula at library-build time".
const std::vector< int > &	getCharges () const
	Return the list of charge states to register for this target.
const std::vector< double > &	getRTs () const
	Return the expected retention times (one library transition per entry).
const std::vector< double > &	getRTRanges () const
	Return the RT tolerance per rts_ entry (or a single broadcast value, or empty for the algorithm default).
const std::vector< double > &	getIsotopeDistribution () const
	Return the pre-computed isotope-intensity distribution (or empty / [0] for runtime computation from formula).
const std::vector< double > &	getIonMobilities () const
	Return the optional ion-mobility values per rts_ entry (or a single broadcast value, or empty to disable IM filtering).
const std::string &	getAdduct () const

Private Attributes
std::string	name_
	Target name; used as the name meta value and in the auto-generated library ID.
std::string	formula_
	Molecular formula; empty if the caller only provides mass_.
double	mass_
	Monoisotopic mass; <= 0 means "compute from @c formula_".
std::vector< int >	charges_
	Charge states to register; entries == 0 are dropped at library-build time.
std::vector< double >	rts_
	Expected retention times; one library transition per entry.
std::vector< double >	rt_ranges_
	RT tolerance per rts_ entry; one-element broadcasts, empty falls back to the algorithm default.
std::vector< double >	iso_distrib_
	Optional pre-computed isotope-intensity distribution; empty (or [0]) triggers computation from formula_.
std::vector< double >	ion_mobilities_
	Optional ion-mobility values per rts_ entry; one-element broadcasts, empty disables IM filtering.
std::string	adduct_
	Adduct string (e.g. "M+H;1+", "M+Na;1+", "M-H;1-"). Empty lets downstream logic infer defaults from charge polarity.

Detailed Description

One target compound for the FeatureFinderAlgorithmMetaboIdent assay library.

Plain data container. No validation is performed in the constructor or accessors — the contract below is enforced when the compound is consumed by FeatureFinderAlgorithmMetaboIdent::run via the internal addTargetToLibrary_ helper. Compounds that violate the contract are silently dropped with an OPENMS_LOG_ERROR message at run time:

• Either mass > 0 or a non-empty formula is required (one of the two must be present so the m/z can be derived).
• rts must be non-empty.
• For each entry in charges, the charge state must be non-zero.
• rt_ranges (when provided) and ion_mobilities (when provided) must have either 1 entry (broadcast to every RT) or exactly rts.size() entries.

The struct stores the per-target data verbatim; the downstream library builder fills in defaults (e.g. RT range 0.0, ion mobility sentinel -1.0 for "no IM filter") and computes the isotope distribution from formula when iso_distrib is empty or its first entry is 0.

Constructor & Destructor Documentation

FeatureFinderMetaboIdentCompound()

FeatureFinderMetaboIdentCompound ( const std::string &  _name, const std::string &  _formula, double  _mass, const std::vector< int > &  _charges, const std::vector< double > &  _rts, const std::vector< double > &  _rt_ranges, const std::vector< double > &  _iso_distrib, const std::vector< double > &  _ion_mobilities = {}, const std::string &  _adduct = ""  )

inline

Construct a target compound by aggregating its identification data.

Parameters

[in]	_name	Target name (used as a tag in the resulting assay library).
[in]	_formula	Molecular formula (e.g. "C12H22O11"); empty when only _mass is provided.
[in]	_mass	Monoisotopic mass; <= 0 means "derive from @p _formula".
[in]	_charges	Charge states to register for this target; each non-zero entry produces one library transition.
[in]	_rts	Expected retention times (one library entry per RT). Must be non-empty when the compound is fed into FeatureFinderAlgorithmMetaboIdent::run.
[in]	_rt_ranges	RT tolerance per RT (parallel to _rts); a one-element vector is broadcast, an empty vector uses the algorithm default.
[in]	_iso_distrib	Pre-computed isotope-intensity distribution; empty (or first entry 0) triggers computation from _formula at library-build time.
[in]	_ion_mobilities	Optional ion-mobility values (parallel to _rts); a one-element vector is broadcast, an empty vector disables IM filtering for this target.
[in]	_adduct	Adduct string (e.g. "M+H;1+", "M+Na;1+"); empty lets downstream logic infer defaults from charge polarity.

Member Function Documentation

getAdduct()

const std::string & getAdduct ( ) const

inline

getCharges()

const std::vector< int > & getCharges ( ) const

inline

Return the list of charge states to register for this target.

getFormula()

const std::string & getFormula ( ) const

inline

Return the molecular formula (may be empty if only mass was provided).

getIonMobilities()

const std::vector< double > & getIonMobilities ( ) const

inline

Return the optional ion-mobility values per rts_ entry (or a single broadcast value, or empty to disable IM filtering).

getIsotopeDistribution()

const std::vector< double > & getIsotopeDistribution ( ) const

inline

Return the pre-computed isotope-intensity distribution (or empty / [0] for runtime computation from formula).

getMass()

double getMass ( ) const

inline

Return the monoisotopic mass; <= 0 means "compute from @c formula at library-build time".

getName()

const std::string & getName ( ) const

inline

Return the target name.

getRTRanges()

const std::vector< double > & getRTRanges ( ) const

inline

Return the RT tolerance per rts_ entry (or a single broadcast value, or empty for the algorithm default).

getRTs()

const std::vector< double > & getRTs ( ) const

inline

Return the expected retention times (one library transition per entry).

Member Data Documentation

adduct_

std::string adduct_

private

Adduct string (e.g. "M+H;1+", "M+Na;1+", "M-H;1-"). Empty lets downstream logic infer defaults from charge polarity.

charges_

std::vector<int> charges_

private

Charge states to register; entries == 0 are dropped at library-build time.

formula_

std::string formula_

private

Molecular formula; empty if the caller only provides mass_.

ion_mobilities_

std::vector<double> ion_mobilities_

private

Optional ion-mobility values per rts_ entry; one-element broadcasts, empty disables IM filtering.

iso_distrib_

std::vector<double> iso_distrib_

private

Optional pre-computed isotope-intensity distribution; empty (or [0]) triggers computation from formula_.

mass_

double mass_

private

Monoisotopic mass; <= 0 means "compute from @c formula_".

name_

std::string name_

private

Target name; used as the name meta value and in the auto-generated library ID.

rt_ranges_

std::vector<double> rt_ranges_

private

RT tolerance per rts_ entry; one-element broadcasts, empty falls back to the algorithm default.

rts_

std::vector<double> rts_

private

Expected retention times; one library transition per entry.